Introduction “igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.”
This procedure will identify sub-networks from a given network, using three clustering algorithms implemented by igraph: fast greedy, walktrap, and edge betweenness. The sub-networks will be further analyzed by enrichment analysis for their functional annotation.
Summary
The full network includes 467 nodes and 1496 edges (3.2 edges per nodes). For enrichment analysis, 466 nodes in the network can be mapped to one or more node sets, while there are totally 28850 unique nodes in all node sets. The background of the enrichment analysis has 21426 nodes. The maximum number of edges a node has is 53 and 118 (25.27%) nodes have only one edge.
**Figure 1.** Number of edges per nodes.
Clustering analysis with different algorithms
Fast greedy
**Figure 2A.** Clustering via the fast greedy modularity optimization algorithm.
**Figure 2B.** Individual clusters identified via the fast greedy modularity optimization algorithm.
Table 1. Enrichment analysis of network clusters identified by the fast greedy algorithm.
Cluster Size Core_Member Top_Set Top_OddsRatio Top_PValue Top_FDR
------------------------------------------------- ------------------------------------------ ----------------------------------------------------- ---------------------------------------------------------------------------------------------------------------------- -------------- ----------- --------
[Cluster_1](table/ORA_FastGreedy_Cluster_1.html) [93](table/ORA_FastGreedy_Cluster_1.txt) TP53
h_all_33 21.50 0 1e-07
[Cluster_2](table/ORA_FastGreedy_Cluster_2.html) [44](table/ORA_FastGreedy_Cluster_2.txt) RPS5; RPL19; RPS23; RPL15; RPL4; RPS7; RPL12; RPL10A
491332 216.23 0 0e+00
[Cluster_3](table/ORA_FastGreedy_Cluster_3.html) [40](table/ORA_FastGreedy_Cluster_3.txt) HSP90AA1
1127556 647.85 0 0e+00
[Cluster_4](table/ORA_FastGreedy_Cluster_4.html) [119](table/ORA_FastGreedy_Cluster_4.txt) FYN
hsa05205 20.24 0 0e+00
[Cluster_5](table/ORA_FastGreedy_Cluster_5.html) [28](table/ORA_FastGreedy_Cluster_5.txt) POLR1B; RPLP0
486555 123.41 0 0e+00
[Cluster_6](table/ORA_FastGreedy_Cluster_6.html) [68](table/ORA_FastGreedy_Cluster_6.txt) POLR2A
486891 34.91 0 0e+00
Walktrap
**Figure 3A.** Clustering via the Walktrap community finding algorithm.
**Figure 3B.** Individual clusters identified via the Walktrap community finding algorithm.
Table 2. Enrichment analysis of network clusters identified by the walkgrap algorithm.
Cluster Size Core_Member Top_Set Top_OddsRatio Top_PValue Top_FDR
----------------------------------------------- --------------------------------------- -------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------------------------------- -------------- ----------- ---------
[Cluster_1](table/ORA_Walktrap_Cluster_1.html) [76](table/ORA_Walktrap_Cluster_1.txt) FYN
hsa04810 28.34 0 0.00e+00
[Cluster_2](table/ORA_Walktrap_Cluster_2.html) [46](table/ORA_Walktrap_Cluster_2.txt) TP53; HSP90AA1
c2_cp_BIOCARTA_88 153.25 0 1.55e-05
[Cluster_3](table/ORA_Walktrap_Cluster_3.html) [24](table/ORA_Walktrap_Cluster_3.txt) NOP2
486555 122.00 0 0.00e+00
[Cluster_4](table/ORA_Walktrap_Cluster_4.html) [50](table/ORA_Walktrap_Cluster_4.txt) POLR2A
160950 73.82 0 0.00e+00
[Cluster_5](table/ORA_Walktrap_Cluster_5.html) [42](table/ORA_Walktrap_Cluster_5.txt) RPS5; RPL19; POLR1B; RPS23; RPL15; RPL4; RPLP0; RPS7; RPL12; RPL10A
491332 202.29 0 0.00e+00
Edge betweenness
**Figure 4A.** Clustering via the edge betweenness algorithm.
**Figure 4B.** Individual clusters identified via the edge betweenness algorithm.
Table 3. Enrichment analysis of network clusters identified by the edge betweenness algorithm.
Cluster Size Core_Member Top_Set Top_OddsRatio Top_PValue Top_FDR
------------------------------------------------------ ---------------------------------------------- -------------------------------------------------------------------- ----------------------------------------------------------------------------------------- -------------- ----------- ---------
[Cluster_1](table/ORA_EdgeBetweenness_Cluster_1.html) [40](table/ORA_EdgeBetweenness_Cluster_1.txt) PPARA
160977 68.83 0 0.00e+00
[Cluster_2](table/ORA_EdgeBetweenness_Cluster_2.html) [32](table/ORA_EdgeBetweenness_Cluster_2.txt) HSP90AA1
1127556 855.48 0 0.00e+00
[Cluster_3](table/ORA_EdgeBetweenness_Cluster_3.html) [71](table/ORA_EdgeBetweenness_Cluster_3.txt) RPS5; RPL19; POLR1B; RPS23; RPL15; RPL4; RPLP0; RPS7; RPL12; RPL10A
491332 61.94 0 0.00e+00
[Cluster_4](table/ORA_EdgeBetweenness_Cluster_4.html) [70](table/ORA_EdgeBetweenness_Cluster_4.txt) TP53
493498 10.79 0 2.89e-05
[Cluster_5](table/ORA_EdgeBetweenness_Cluster_5.html) [98](table/ORA_EdgeBetweenness_Cluster_5.txt) FYN
106034 23.18 0 0.00e+00
[Cluster_6](table/ORA_EdgeBetweenness_Cluster_6.html) [69](table/ORA_EdgeBetweenness_Cluster_6.txt) POLR2A
486891 37.15 0 0.00e+00